KAJIAN AWAL APTAMER SEBAGAI BIORESEPTOR UNTUK DETEKSI PROTEIN SPIKE SARS-COV-2

• Main Author: Aji Lumintang, Yunus
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/61968
• Institution: Institut Teknologi Bandung

SARS-CoV-2 is a new strain of Coronavirus that has caused a pandemic since early 2020. The spread of this virus is difficult to control and robust detection system to-date is based on qPCR. Drawbacks of the large scale application of qPCR have made non-PCR diagnostic kits play an important role for contact tracing. Aptamers have a potential to be used as a bioreceptor in non-PCR diagnostic kits due to its specific binding ability like antigen-antibody. This research was an initial study regarding the aptamer potential for SARS-CoV-2 spike protein detection. Aptamer sequence which has been reported to be able to interact with the receptor binding domain (RBD) of spike protein was used as an lead aptamer. Several modifications were made to make new sequences expected to provide its characteristics. These aptamers underwent an in silico study through 2D and 3D structure prediction, molecular docking, and feasibility studies. From six modifications, five of them retained its original 2D structure. 1C-RNA M1-M3 aptamers had docking orientation that were consistent with reported study and the interactions were qualitatively equivalent. The docking position of 1C-RNA M5-M6 aptamers demonstrated the possibility of other binding mode to the RBD of spike protein. Feasibility study toward trimeric spike protein showed that 1C-RNA M1, M2, M3, and M5 aptamers did not form a clash with other spike monomers, while 1C-RNA M6 were predicted to have minor clash. All modified aptamers retained its original 2D structure following the insertion of poly-A-tail at 3’end. From these results, five aptamers were recommended for further in vitro study.